chr5-112697347-G-C

Position:

• chr5-112697347-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.41 in 151,218 control chromosomes in the GnomAD database, including 14,922 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (14922 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.410 AC: 61958 AN: 151100 Hom.: 14920 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.447

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.410 AC: 61972 AN: 151218 Hom.: 14922 Cov.: 31 AF XY: 0.413 AC XY: 30446 AN XY: 73772

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.447

Alfa AF: 0.420 Hom.: 1443

Bravo AF: 0.413

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10051624; hg19: chr5-112033044;